Automatic Updater doesn't always indent old code inside new conditional statements

In some files, the Automatic Updater does not indent old code correctly when new conditionals statements are added. When updating from 3.0.7-PL1 to 3.0.8-RC1, the following files have this issue:

acp_users.php lines 196-213
common.php line 128
functions.php lines 2372-2425, 3517-3519, and 3592-3594, 3601, 3608, 3613
functions_admin.php lines 1163-1177
mcp_queue.php lines 696-705
phpbb_recaptcha_plugin.php lines 316-317
search.php lines 73-74
sqlite.php line 69